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Limit : this week
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231 results • Page
4 of 5
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Views
Votes
Replies
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
6 days ago by
applepie
• 0
0
votes
0
replies
178
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
6 days ago by
Minh
• 0
0
votes
0
replies
177
views
Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"
SCTransform
updated 6 days ago by
Ram
43k • written 6 days ago by
Anisha
• 0
0
votes
0
replies
177
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
5 days ago by
enee
▴ 10
0
votes
0
replies
173
views
Example - Meta Analysis TCGA and DepMap
Meta-Analysis
TCGA
DepMap
updated 6 days ago by
Ram
43k • written 7 days ago by
joseph.landry
▴ 50
1
vote
2
replies
171
views
vg call is time consuming
vg
19 hours ago by
Maxine
▴ 40
0
votes
0
replies
170
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
6 days ago by
sakura
• 0
1
vote
1
reply
169
views
Forum:
Can I use this community for software development?
software-development
updated 2 days ago by
Ram
43k • written 3 days ago by
avpuzanov
• 0
2
votes
1
reply
164
views
Choosing an FC Threshold
statistics
rna-seq
updated 13 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
0
replies
164
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
6 days ago by
Apex92
▴ 280
0
votes
1
reply
164
views
RNA-seq with normalized cpm count
RNA-seq
Deseq2
EdgeR
updated 2 days ago by
Ram
43k • written 2 days ago by
GiV17
▴ 50
0
votes
0
replies
163
views
Tutorial:
Parsing HMMER output
HMMER
updated 5 days ago by
GenoMax
140k • written 5 days ago by
I0110
▴ 130
0
votes
0
replies
163
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
1
reply
162
views
MACS3 or SEACR
MACS3
SEACR
updated 1 day ago by
jared.andrews07
★ 16k • written 2 days ago by
daffodil
▴ 10
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
6 days ago by
mb
• 0
0
votes
1
reply
155
views
Difference in relative abundance between MicrobiomeDB and r phyloseq
phyloseq
updated 3 days ago by
Chris Dean
▴ 390 • written 3 days ago by
benkosta
• 0
1
vote
1
reply
152
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 1 day ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
0
votes
2
replies
151
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
15 hours ago by
Ankit
▴ 500
0
votes
2
replies
148
views
Error with goodSamplesGenes()
R
WGCNA
20 hours ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
146
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
5 days ago by
asmariyaz23
▴ 10
0
votes
1
reply
145
views
NCBI gene data
Variants
NCBI
updated 2 days ago by
GenoMax
140k • written 2 days ago by
chandrakala.m
• 0
0
votes
1
reply
145
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 2 days ago by
zx8754
11k • written 2 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
1
reply
145
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
Mary
• 0
0
votes
2
replies
142
views
novel and know mir156 and mir172
a
updated 13 hours ago by
gayachit
▴ 200 • written 16 hours ago by
Fadmo
• 0
0
votes
1
reply
141
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
0
replies
141
views
Blog:
WGBS vs RRBS
RRBS
DNA-methylation
WGBS
updated 6 days ago by
Ram
43k • written 7 days ago by
Novogene
▴ 410
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
4 days ago by
rheab1230
▴ 140
0
votes
1
reply
139
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 2 days ago by
Ram
43k • written 3 days ago by
Sony
▴ 10
0
votes
1
reply
136
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
3
replies
135
views
calculate mismatch rate from VCF file
rate
VCF
mismatch
updated 2 hours ago by
Pierre Lindenbaum
160k • written 10 hours ago by
Dora
▴ 10
0
votes
1
reply
127
views
Can I have multiple active GDC download tokens?
TCGA
updated 2 days ago by
GenoMax
140k • written 2 days ago by
mrk
• 0
0
votes
1
reply
126
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
updated 7 hours ago by
kayah
• 0 • written 9 hours ago by
Nitin
• 0
0
votes
1
reply
126
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 20 hours ago by
Ram
43k • written 22 hours ago by
Hajar
• 0
0
votes
0
replies
125
views
Job:
Post-doctoral positions in computational biomedicine
data-science
biomedicine
machine-learning
updated 2 days ago by
Ram
43k • written 2 days ago by
pandey.gaurav
▴ 200
3
votes
0
replies
123
views
Herald:
The Biostar Herald for Monday, March 25, 2024
herald
3 days ago by
Biostar
2.6k
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 2 days ago by
GenoMax
140k • written 2 days ago by
houssi301
• 0
0
votes
0
replies
114
views
News:
Online course: Introduction to GWAS
GWAS
Imputation
StatisticalPower
4 days ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
113
views
How can I remove duplicate SNP?
plink
updated 22 hours ago by
iraun
6.2k • written 22 hours ago by
Zhennan
• 0
1
vote
0
replies
108
views
checkm lineage.ms output file
checkm
lineage
3 days ago by
A_heath
▴ 160
0
votes
0
replies
106
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
2 days ago by
Yingying
• 0
0
votes
1
reply
105
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 16 hours ago by
Mensur Dlakic
★ 26k • written 23 hours ago by
Ricard
• 0
0
votes
0
replies
105
views
t2t Reference gtf file
t2t
2 days ago by
Emre
• 0
0
votes
0
replies
104
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
PBC
▴ 10
0
votes
0
replies
103
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
barrypraveen
▴ 130
0
votes
1
reply
100
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 20 hours ago by
Yogi
▴ 70 • written 21 hours ago by
Ronin
• 0
0
votes
0
replies
99
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
0
votes
0
replies
99
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
0
votes
0
replies
99
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 3 days ago by
Carlo Yague
8.6k • written 3 days ago by
anne
• 0
1
vote
0
replies
96
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
2 days ago by
mrazib0210
▴ 10
231 results • Page
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Comment: Volcano Plot Output Inquiry: Graphs Facing Down
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
Crispr-cas9 screen analysis mageck
Comment: Issue with making local BLAST database
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
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Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Comment: Issue with making local BLAST database
by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
Comment: Flow Cytometry Data Analysis by Seurat
by
ATpoint
81k
> I think Seurat is suitable for our purpose (e.g. conducting dimensional reduction of the data such as tSNE), but does it make sense? No…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
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